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Allison Burns

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This resume was made with the R package pagedown.

Last updated on 2022-04-05.

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Allison Marie Burns

PhD, Bioinformatician and Genomicist

I am a bioinformatician and scientist with more than 8 years of experience working with NGS datasets. I am passionate about using multi-omics approaches to explore the genetics of diseases and to develop novel therapeutics to ameliorate those disorders. My motivation is to leverage my skills as part of a team to successfully conduct and communicate data-drive research.

Experience

Doctoral Researcher and Bioinformatician

Laboratory of Neuroepigenetics - Gräff Lab

EPFL

2022 - 2016

  • Integrated multi-omics datasets to determine mechanisms of HDACi treatment in memory amelioration
  • Designed, performed and analyzed molecular and bioinformatic experiments
  • Created and managed analysis pipelines for myself and colleagues
  • Advised colleagues on best methods for NGS sample and library preparation
  • Maintained and organized computational storage needs for the lab

Bioinformatician / Research Associate

Baumann Laboratory

Stowers Institute for Medical Research

2016 - 2013

  • Analyzed RNA-seq data and performed transcriptome assembly with Trinity
  • Performed basic tissue culture and molecular experiments

Undergraduate Researcher

Bradshaw-Holzapfel Laboratory

University of Oregon

2012 - 2010

  • Measured animal fitness in extreme light environments
  • Studied the evolutionary divergence of circadian clock genes in mosquitos

Education

Ph.D. in Neuroscience

Lausanne, Switzerland

École Polytechnique Fédérale de Lausanne

2022

Title: Epigenetic memory aids: Synaptic and molecular effects of HDAC
inhibition that support memory formation

M.Sc. in Bioinformatics

Eugene, Oregon, USA

University of Oregon

2013

Title: Effects of the splicing inhibitor, Isoginkgetin, on human Telomerase RNA

B.Sc. in Biology

Eugene, Oregon, USA

University of Oregon

2012

Project: Evolutionary genetics of geographical variation, seasonal development and circadian timing in the North American mosquito species, Wyeomyia smithii

Technical Skills

Bioinformatics and NGS Data Analysis

  • R/Bioconductor (highly proficient), Bash (proficient), Python (competent)
  • Data wrangling, statistical analysis, and data visualization in R (tidyr, dplyr, ggplot, etc)
  • Quality control and processing of sequencing data (FastQC, STAR alignment, Bowtie suite, CellRanger, etc)
  • Analysis and integration of RNA-seq (edgeR, DESeq2), scRNA-seq (Seurat, RNAvelocity) and ChIP-seq (DiffBind)
  • Exploration and interpretation of complex omics datasets (BiomaRt, Gprofiler2,TopGO, Cytoscape, etc)
  • Ability to link transcription and epigenetic data analysis to behavioral phenotypes

N/A

Computing Experience

  • Version control with git and Github
  • Software download and maintenance (conda, homebrew, etc)
  • Experience using cloud computing and high performance clusters for analysis and storage of large datasets

N/A

Communication

  • Documentation with Rmarkdown (Pagedown and KnitR), Emacs Org Mode and Jupyter Notebooks
  • Presenting and communication (Microsoft Office and Adobe Suite) with scientists in my field and unrelated fields
  • Excellent written communication in the form of manuscript and thesis writing
  • Website development (R Blogdown and Wordpress with basic markdown and HTML)

N/A

Laboratory Techniques

  • Techniques for NGS experimentation (nuclear and RNA extractions, ChIP, library preparation, etc)
  • Molecular Biology Techniques (FANS, Western, qPCR, etc)
  • Animal Handling (mouse and insect)

N/A

Courses and Training

Genome variant analysis

Swiss Institute of Bioinformatics

N/A

2022

Scientific writing for biomedical articles

École Polytechnique Fédérale de Lausanne

N/A

2021

Advanced topics in single-cell transcriptomics

Swiss Institute of Bioinformatics

N/A

2020

Genetic and epigenetic mechanisms underlying brain disorders

FENS-Hertie Winter School 2019

N/A

2019

Science and Engineering Teaching and Learning

CAPE-Teaching Support Centre, EPFL

N/A

2018

Image Processing for Life Scientists

École Polytechnique Fédérale de Lausanne

N/A

2016

High Performance Computing (HPC) in Life Sciences

Swiss Institute of Bioinformatics

N/A

2016

Teaching and Mentoring

Robust data analysis: an introduction to R

Designed and taught introduction to R in an afternoon lecture

Open Science in Practice Summer School

2019

Project Supervisor for Bachelor Students

Mentored students for projects (3wks - 1yr) involving lab techniques and bioinformatic analysis

EPFL

2017-21

Laboratoire Intégré en Sciences de la Vie I/II

Taught and demonstrated lab techniques and analysis to first year bachelor students

EPFL

2017-19

Selected Presentations

Federation of European Neuroscience Society Forum 2020 (virtual poster)

Testing the theory of Epigenetic Priming in Fear Memory Conditioning

Glasgow, Scotland

2020

FENS-Hertie Winter School 2019 (poster)

Testing the theory of Epigenetic Priming in Fear Memory Conditioning

Obergurgl, Austria

2019

Society For Neuroscience Annual Meeting 2019 (poster)

Testing the theory of Epigenetic Priming in Fear Memory Conditioning

Chicago, Illinois, USA

2019

Molecular and Cellular Cognition Society 18th Annual Meeting (talk)

Testing the theory of Epigenetic Priming in Fear Memory Conditioning

Chicago, Illinois, USA

2019

Single Cell Biology Symposium (talk)

Variations of epigenetic priming across hippocampal cell types during memory formation

Lausanne, Switzerland

2019

Lemanic Neuroscience Annual Meeting (poster)

Testing the theory of Epigenetic Priming in Fear Memory Conditioning

Diableret, Switzerland

2019

Neural Circuits and Behavior (talk)

HDAC inhibitors that prime in fear memory conditioning

Lausanne, Switzerland

2018

Federation of European Neuroscience Society Forum 2018 (poster)

Epigenetic Priming and Fear Memory Conditioning

Berlin, Germany

2018

Functional Genomics Symposium (talk)

Epigenetic priming in fear memory conditioning

Lausanne, Switzerland

2018

Publications

The HDACi inhibitor CI-994 acts as a molecular memory aid by enhancing synaptic and intra-cellular communication after learning

Allison M. Burns, Mélissa Farinelli-Scharly, Sandrine Hugues-Ascery, Jose Vicente Sanchez-Mut, Giulia Santoni,Johannes Gräff
BioRxiv

N/A

2021

A thalamo-amygdalar circuit underlying the extinction of remote fear memories

Bianca A. Silva, Simone Astori, Allison M. Burns, Hedrik Heiser, Lukas van den Heuvel, Giulia Santoni,
Maria Fernanda Martinez-Reza, Carmen Sandi, Johannes Gräff
Nature Neuroscience

N/A

2021

Cognitive epigenetic priming: Leveraging histone acetylation for memory amelioration

Allison M. Burns, Johannes Gräff
Current Opinion in Neurobiology

N/A

2020

A cFos activation map of remote fear memory attenuation

Bianca A. Silva, Allison M. Burns, Johannes Gräff
Psychopharmacology

N/A

2018

Human Telomerase RNA Processing and Quality Control

Chi-Kang Tseng, Hui-Fang Wang, Allison M. Burns, Morgan R. Schroeder, Martina Gaspari, Peter Baumann
Cell Reports

N/A

2015

Leadership and Outreach

Pint of Science

Webmaster (https://pintofscience.ch/)

N/A

2019-22

EDNE Neuroscience Student Association

Event Organizer

N/A

2019

R-Ladies Lausanne

Member

N/A

2018-21

Letters to a Pre-scientist

STEM Professional

N/A

2018-21

Association of Doctoral Students in Life Sciences (ADSV)

Webmaster & Head of Coaches

N/A

2018-20